Transcription factors represent an important as well as challenging class of proteins for development of small molecule inhibitors. Because of their function as nodes in a wide swath of signaling pathways and their well-documented importance for tumor growth and metastasis, they are particularly attractive targets for cancer therapy.
Core binding factor (CBF) is a heterodimeric transcription factor composed of a DNA-binding RUNX subunit (encoded by one of three genes: RUNX1, RUNX2, or RUNX3) and a non-DNA-binding CBFβ subunit, which increases the affinity of RUNX proteins for DNA. All three RUNX proteins as well as CBFβ have been shown to be critical regulators of specific developmental pathways. RUNX1 and CBFβ are essential for definitive hematopoiesis, where they regulate expression of genes associated with proliferation, differentiation, and survival of stem and progenitor cells. RUNX2 is essential for normal bone formation by way of transcriptional regulation of genes critical for bone development. Both RUNX1 and RUNX3 play key roles in neuronal development.
Based on their critical roles in normal development, RUNX proteins and CBFβ are targets of alteration in a number of cancers. Both RUNX1 and CBFβ undergo chromosomal translocations in a subset of acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) patients where the corresponding fusion proteins have clearly been shown to be drivers of disease. For the fusion proteins AML1-ETO and TEL-AML1, the binding of the fusion proteins to CBFβ has been shown to be essential for transformation. RUNX1 is mutated in a subset of AML and myelodysplastic syndrome (MDS) patients.
In addition, RUNX1 has recently been implicated in a number of epithelial cancers. Recent literature also strongly implicates the RUNX family of transcription factors as playing a key role in lung cancer progression, where RUNX cooperates with GATA2 to regulate genes important in growth and survival of lung cancer cells. Altered expression of RUNX2 has also been implicated in breast and prostate cancers. Silencing of RUNX3 by DNA methylation has been linked to intestinal and lung cancers. Due to the importance of these proteins for normal development as well as in a variety of cancers, small molecules that can modulate their activity are useful tools to address function and test new therapeutic approaches.
Small molecule inhibitors of protein-protein interactions, particularly in the context of transcription factors, is still a relatively nascent field, in part due to the long and widely held belief that this class of interactions is “undruggable,” i.e., targeting such interactions would have a very low likelihood of success. With an increasing number of success stories of small molecule inhibitors affecting protein-protein interactions, including transcription factors, this paradigm is clearly changing. In addition, the recent development of small molecule inhibitors of epigenetic signaling proteins, such as the BRD4 or EZH2 inhibitors, clearly indicate that small molecule modulation of transcription, in particular, is a potentially powerful approach to cancer treatment.
We recently reported in U.S. Pat. No. 8,748,618 inhibitor compounds that selectively bind to the abnormal transcription factor CBFβ-SMMHC fusion protein and inhibit its binding to the Runt domain of RUNX proteins. This binding to CBFβ-SMMHC results in delay of the type of AML that involves the chromosome inversion inv(16)(p13q22) (inv(16) leukemia). The disclosed compounds inhibited proliferation of inv(16) leukemia cells, making the compounds useful for treatment of inv(16) leukemia. There is no evidence that CBFβ-SMMHC fusion protein is present in any type of leukemia other than inv(16) leukemia or any other type of cancer.
There is thus a long-felt need in the art for compositions and methods useful for treating RUNX-signaling-dependent cancers that express wild-type CBFβ, i.e., those cancers that do not involve expression of the CBFβ-SMMHC fusion protein.